def setUp(self):
DB.drop_database('atlas-test')
self.pg = AlleleGenerator(
reference_filepath="atlasvar/data/NC_000962.2.fasta")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def run(parser, args):
db_name = 'atlas-%s' % (args.db_name)
DB = connect(db_name)
if args.verbose:
logger.setLevel(level=logging.DEBUG)
else:
logger.setLevel(level=logging.INFO)
al = AlleleGenerator(
reference_filepath=args.reference_filepath,
kmer=args.kmer)
_variant_ids = get_non_singelton_variants(db_name)
total = Variant.snps(id__in=_variant_ids).count()
N = 100
pages = math.ceil(total / N)
for page in range(pages):
logger.info("%i of %i - %f%%" %
(page*N, total, round(100*(page*N)/total, 2)))
for variant in Variant.snps(id__in=_variant_ids).order_by("start").skip(N*page).limit(N):
# for variant in Variant.snps().order_by("start"):
variant_panel = make_variant_probe(al, variant, args.kmer, DB=DB)
for i, ref in enumerate(variant_panel.refs):
sys.stdout.write(
">ref-%s?var_name=%snum_alts=%i&ref=%s&enum=%i\n" %
(variant_panel.variant.var_hash, variant.var_name[:100], len(
variant_panel.alts), variant_panel.variant.reference.id, i))
sys.stdout.write("%s\n" % ref)
for i, a in enumerate(variant_panel.alts):
sys.stdout.write(">alt-%s?var_name=%s&enum=%i\n" %
(variant_panel.variant.var_hash, variant.var_name[:100], i))
sys.stdout.write("%s\n" % a)
def __init__(self, bigsi, reference):
self.bigsi = bigsi
self.reference = reference
self.al = AlleleGenerator(reference_filepath=self.reference,
kmer=self.bigsi.kmer_size)
def __init__(self, cbg, reference):
self.cbg = cbg
self.reference = reference
self.al = AlleleGenerator(reference_filepath=self.reference,
kmer=self.cbg.kmer_size)
def test_panel_generator(self):
pg = AlleleGenerator(
reference_filepath="atlasvar/data/BX571856.1.fasta")
assert pg.ref is not None
class TestSNPAlleleGenerator():
def setUp(self):
DB.drop_database('atlas-test')
self.pg = AlleleGenerator(
reference_filepath="atlasvar/data/BX571856.1.fasta")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file",
reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref",
md5checksum="sre",
reference_sets=[
self.reference_set])
def test_panel_generator(self):
pg = AlleleGenerator(
reference_filepath="atlasvar/data/BX571856.1.fasta")
assert pg.ref is not None
def test_simple_variant(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
panel = self.pg.create(v)
assert panel.refs == [
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT"]
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT"]
assert self.pg._calculate_length_delta_from_indels(v, []) == 0
assert v.is_indel is False
def test_simple_variant2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
panel = self.pg.create(v)
assert panel.refs == [
"GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC"]
assert panel.alts == [
"GATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGATC"]
def test_simple_variant_invalid(self):
with assert_raises(ValueError) as cm:
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=31,
alternate_bases=["T"])
panel = self.pg.create(v)
def test_simple_variant_start(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=1,
alternate_bases=["T"])
panel = self.pg.create(v)
assert panel.refs == [
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT"]
assert panel.alts == [
"TGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT"]
def test_simple_variant_end(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=2902618,
alternate_bases=["T"])
panel = self.pg.create(v)
assert panel.refs == [
"TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTAT"]
assert panel.alts == [
"TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTTT"]
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=2902616,
alternate_bases=["C"])
panel = self.pg.create(v)
assert panel.refs == [
"TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTAT"]
assert panel.alts == [
"TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTCTAT"]
def test_simple_variant_with_nearby_snp(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
panel = self.pg.create(v, context=[v2])
assert panel.refs == ["CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGAT"]
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTGAT"]
def test_simple_variant_with_multiple_nearby_snps(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"])
panel = self.pg.create(v, context=[v2, v3])
assert panel.refs == ['CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT',
'CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGAT',
'CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTGAT',
'CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTGAT']
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTGAT"]
def test_simple_variant_with_multiple_nearby_snps2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"])
v4 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["T"])
v5 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["A"])
assert sorted(self.pg._split_context([v, v3, v4])) == sorted(
[[v, v4], [v, v3]])
assert (self.pg._split_context([v3, v4])) == [[v4], [v3]]
assert (self.pg._split_context([v, v3, v4, v5])) == [
[v, v4, v5], [v, v3, v5]]
panel = self.pg.create(v, context=[v2, v3, v4, v5])
assert sorted(panel.refs) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGAAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGAATTCAAATTTCATAACATCACCATGAGTTTGAT"])
assert sorted(
panel.alts) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGATATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGATTTCAAATTTCATAACATCACCATGAGTTTGAT"])
def test_simple_variant_with_multiple_nearby_snps(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["T"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
v5 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["G"])
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["G"])
v4 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=30,
alternate_bases=["T"])
panel = self.pg.create(v, context=[v2, v3, v4, v5])
assert sorted(panel.refs) == sorted([
"CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTAATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTATTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCAGTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGAGTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTAGTCAAATTTCATAACATCACCATGAGTTTGAT"])
assert sorted(
panel.alts) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTTTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCTGTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGGTGTCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGTTGTCAAATTTCATAACATCACCATGAGTTTGAT"])
class TestLargeINDELAlleleGenerator():
def setUp(self):
DB.drop_database('atlas-test')
self.pg = AlleleGenerator(
reference_filepath="atlasvar/data/NC_000962.2.fasta")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def test_large_variant(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases=
"AACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACT",
start=1355983,
alternate_bases=[
"ACCGCCCGGTATCTGAGGATTGGTTTTCCACCCAAATACAAGTCGCATTCGCG"
])
panel = self.pg.create(v)
assert "TCGTCAACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACTGGACC" in panel.refs
assert panel.alts == [
"TCGTCACCGCCCGGTATCTGAGGATTGGTTTTCCACCCAAATACAAGTCGCATTCGCGGGACC"
]
def test_large_variant2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases=
"AACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCAC",
start=1355983,
alternate_bases=[
"ACCGCCCGGTATCTGAGGATTGGTTTTCCACCCAAATACAAGTCGCATTCGC"
])
panel = self.pg.create(v)
assert "TCGTCAACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACTGGACC" in panel.refs
assert panel.alts == [
"TCGTCACCGCCCGGTATCTGAGGATTGGTTTTCCACCCAAATACAAGTCGCATTCGCTGGACC"
]
def test_large_variant3(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases=
"TCGTCAACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACTGGACC",
start=1355978,
alternate_bases=[
"TCGTCAACGCCCGGTATCTGAGGATCGGTGTTCTCACCCAATACAAGTCGCATTCACTGGACC"
])
panel = self.pg.create(v)
assert "CAAACCTCGTCAACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACTGGACCGCCATA" in panel.refs
assert panel.alts == [
"CAAACCTCGTCAACGCCCGGTATCTGAGGATCGGTGTTCTCACCCAATACAAGTCGCATTCACTGGACCGCCATA"
]
def test_very_large_variant3(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases=
"TCGTCAACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACTGGACCGCCAT",
start=1355978,
alternate_bases=[
"TCGTCAACGCCCGGTATCTGAGGATCGGTGTTCACCCAATACAAGTCGCATTCACTGGACCGCCAT"
])
panel = self.pg.create(v)
assert "AAACCTCGTCAACGCCCGGTATCTGAGGATCTGTGTTCTCACCCAATACAAGTCGCATTCACTGGACCGCCATATCTCG" in panel.refs
assert panel.alts == [
"CAAACCTCGTCAACGCCCGGTATCTGAGGATCGGTGTTCACCCAATACAAGTCGCATTCACTGGACCGCCATATCTCGC"
]
def test_large_insertion(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=2352065,
alternate_bases=[
"CCTCGCCTGGGCTGGCGAGCAGACGCAAAATCCCCCGCACGCCCGGCGTGTCGGGGGATTTTGCGTCTG"
])
panel = self.pg.create(v)
assert "AGCTCGGCCAGCTCAGTCACGTCGCCGCCGCCTCGCCAGTTGACCGCGCCCGCTCGCGGCTAG" in panel.refs
assert panel.alts == [
"AAGTCGTCGAGCGAGAACGGTAGTTCCGCGGTGAACCGGTCCAGCTCGGCCAGCTCAGTCACGTCGCCGCCGCCTCGCCTGGGCTGGCGAGCAGACGCAAAATCCCCCGCACGCCCGGCGTGTCGGGGGATTTTGCGTCTGCTCGCCAGTTGACCGCGCCCGCTCGCGGCTAGCGGGCCTACGTGACGTCGTCATGAGATCCGATGACCGATGGC"
]
def test_large_var1(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases=
"CGCGGGAGTAGAACGATCGCCAAGTGGTCGGTCTTGGCTGCCCACTTCATCCCCGGCGCCACCGGCAGGTCTCGCGGTCATCTCGACCAACGGAGGGCCGTCGGTGGTTCGTATCCGGCCAAGAACGGCGAGAACGGTTTGTGCCTCTATGCCAGGGTGAATGTCTCATCTCCCAGGCGGACGGTGATATCCAGTTCTCCGCCAAGAGCGGACACGTATTTGCGCAGTGTGTTGACCTGTGCGGAGCCGATGTCGCCGTTCTCGATGCTGGATACCCGGCTCTGCCGGATGTGCGCCAGCGCAGCCACCTGGACCTGGGTGAGTGACTGAGCCGCGCGCAGCTCCCGGAGCCGGAATGCCCGCACTTCATCGCGCATTCGTGCCTTGTGCCGGTCCACCGCCTCCCGGTTAACGGGACGTACGGCGTCCATGTCCCGTAGTGTCATCGCCATCGTGCCACTTACCCTTTCTTGCGCTTGCGCCTCTTTGGCTTCGTGTCCTCGAACTGTGCGAGATGTTCGGCAAACATCTCATCGGCCGCTTTGATCTTCTCGTCGTACCACTGGGTCCACCGCCCGGCCTTGTTACCGGCGGCCAGCATGATCGCCTGCCGCGCCGGGTCGAAGGCGAACAGAATGCGGACCTCGGACCGCCCTTGTGATCCTGGACGCAGCTCCTTCATGTTCTTGTGGCGCGACCCACGCACCGTGTCCACCAGAGGACAGCCAAGTGCGGGGCCCTCTTCCTCGAGAACCTCGATAGCTGCGAACACCAATTCGTAGGTCTCTCGGTCCAAGCCGTTGAGCCAGGCGGAGATGCGCTCCACATCCGCCGTCCACCCCACAGAGTCGCAGAGTAGCGCGATACGCGATATCACACAAGGGTGATATTCCTCCGGGTAAGAGCAGCGGGCGACGGGGCTACCGTCGAGGAAATGCCGGCAGGCGAGGACGGACTCTGCGCACCCGGGCCGTTGAAACAGTAGCCTGTGCCAGGCCGAGAATTCATCCCCACGTATGAGGCAGTACAGTGCGCCGCCGTGCGCGTTCTCCCATGGAACGTTCACGGGCTCCCGTGGATGACAGGCGTTTCATGAACGCCAGCGCCGCCGCAACCCGACCGAAAGCGGTTGACCCCAAGGAGAGCTGGAAGTCGAGGCCACCACCTTCGCCGCGGAGTTGCTCATGCCCGAGAGCGAGACTCGTCCCGAAATACGCCGGCTCGATTTCGGCAAGTTGCTCGAACTGAAGCGGGAATGGGCGTCGACCCGCTCGACCAGCCCCAGCCGGGTGACCAGCCCCAGCCGGGTGACCAGCCGATGCACCGCGGCGATCCCACCGAAGCCGGTGGCATCGATGTTGGCGCCGACCTCGTAGCGCACCGCGCCCGAACCCAGCATCGGCCTGGGCTGCGCCGCCCAGCGTCCAGCCCGCGCGTGCCGCGCCGCCACCCTGCGCCCTCGGCGTGTGATGTTTCGCCGACTCTGTTCATGGGTTATCTTCTTCACCACAAAGGCCTTTCCTGCTGGGCTGTGTTGAGGTCGCAAACCCAGCCAGGGTAAGGCCTTTGGCCTCTCCTACCCGGCCGACACGCTTACTGAAGGCCTAGTCTAGGCAGGCCATTCAATCTGCGGAATCGAAAAATTCGGTTCCAGCCTGCTCGTTTCCTTTCCGACAGCGATCTGACGTTGCGTAACGTCATTTGTACGGACTCTTTTAGCGGCATTGATTTCAGATGCCAACGCCGTCTGTGCTGTAGCGCCGATTGGCCGAAACTGTAAATTTGTATGATTATTTAAATCTTTGACGAACACGCGCCACAAACGTACTATCTCTTTGGCAAAGTCCACCGGCATCTCATTCAACGGTTTTGTTTGCGCGTGGTCGTCATATGTTGGTAACTGTGTAACCGGCCGCCTATCTTGCGCGTGCATCATATGACTATGAATCGGCCTTCTCCAGTGAAATTGATACAAGATCGATCCGATAAGCGGTACCTTGTACACAGTGCAATTGTAGTAATTCGCGTTTTGTCCTACGCTTGTATTCTGCGTGAAGAATTCA",
start=2266659,
alternate_bases=[
"CACGCGAGTTGTAGATGATCGTTGAGTGGTCTTGCTTGGACTTCCATTTCATCTTTTCGACGCGCCAGGTCTCGCGGTCCTCCGGATCTGCGCCCGGTTTGAGTTGCACATCAAGGGGATACGGCTTGACCGACTCGTAGCCGACATGTAAGTCGGCTAGTTTCCGGCCGGCGCTGGCGAGCTGGTCGAAGCGTTCGCGGGTCTCCGGTGTTGGGATGTGCGGGAGCATCTTCTTGAGGTCAGCGGCGTATTTTGTGCGGTAGGCGGGGTCATGCAGCAGGCCGTAGACGTAGTAGAAGATGTCGTCTTTGGTGACTTGGTCGCCGATCGTGTCGCGGTAGAGCTTGAGGATGACGCCGGTGATGTTGTCGACGCGGCGGTAGCCGTGGTCGTCTACTTCGGCGTTGGTGGTGGACTCGAAATCGAGTTCGCCGTCACGTGGTTCGGTCTTCTCGTAGGTCCAGCGCGGGAAGAATTGACCGTTGCTTGAGCCCCAGAATGCGAGATCGGGGATAGCGTTTAGCATCAGACACGAGAAGGGCTTGTCTGAGCCCATGCCAACCACGTAGTAACCGACATTCCCGTGCTCCGGCGTCGGAAACATCGACGGAAGCTGGTAGGTACAGTTGTTGAGCTGCTGGTTGGGGTCGAGGTAGGCGTGCTCTTTCGTAAATGGTCGGTACGTGCCGAGCCGCATTCCCGCGGGAGCGAATTCGATGCGAATGCCTTGTGCCACTTGCCGCTTGTTGATGCGGTCCCAGCTGAACTTGGCCGAGTCCACGGTAATGAGGGCGTCAACCGGCGGGGTCTTGGCGTCCCTTCCGCGGATCTCGTTGATCCGGTCGACCTCCGAGTTGTAGAAGTCGATCGTGCGTCCGATGTTGGCCTCGAGCGCACCACGTGAAAAGTTGTAACACCACGCATCCCGGCTGGTCTTCAAGCCCGCGGAATAGTTCGCGAAGACACGTGTCACGTCAAGAGCAGCCTTCTTGTCGCCGATAACCGGCCACGCGCTGAACGCGTCGTCGCGTTGGTTGACCCAGTCACCGTGCAAGTTGGGTGTGACTGTCTGCCATTCCACCGTGTCGAGGTAGCCGTCGCCGACGATCCGCAACTTCTCCTCGCGACTCAGGTAATCGCCGATGTCGCGGTAAAGGACATCGCATGGCCCGCTGTGCTTCGGATCCTTGATGCCAAGGAAGATCGCCACCGTGTTGCGACTCCCCCCGCCAAAGACCTTGCCGCCTTCCTGGCGTGAGAGTTCCCCAGCTGTGCGCTGGTTCCCCCGCAGGTTGTACACATATACCGCCGCGTAGTCGTCGGCGAGCGACAACCGCATGCCGTCTGCCGTGTTGCCGTCTATGTACCCACCATTGGAGACGAATCCGACAACACCGTTGTCACCAATGCGGTCGGTCGCCCACCGGAACGCGCGAATATACGAGTCGTACAGGCTGTTCTTCAGCTGCGCCGTCGACCGCTTCGCGTACGTCTGCTCAATCCGCCCGTCCAACGTCGGATACTTCACGTTGGCGTTCAGGTCGTTCGCGCTGCTCTGCCCCACCGAGTACGGCGGATTCCCGATGATCACGCTGATCGGCGTCGCCAGCTGTCGCAAGATCCGAGCGTTGTTGTACGGGAACATGATCGCGTCCATCGAGTCCCCGGCTTCGGAAATCTGGAACGTGTCGGCCAGCGCCATCCCGGGGAACGGCTCATAGGCGTCGGCGTCGGCGGTCTTGCCCGCCAAAGCATGGTAGGTCGACTCGATGTTCACCGCGGCGATGTAGTACGCCAGCAGCATGATCTCGTTGGCGTGCAGCTCTTGCGAGTACTTTCGGGTGAGGTCGGCGGCCGTGATCAGGTCGGACTGCAGCAGCCGGGTAATGAATGTGCCCGTCCCGGCGAAGCCGTCCAGAATATGCACGCCCTCGTCGGTCAGCCCGCGCCCGAAATGCTTGCGCGACACGAAATCAGCCGCCCGCACAATGAAGTCCACGACCTCGACCGGCGTGTACACGATCCCCAGCGCCTCGGCCTGCTTCTTGAAGCCGATGCGGAAGAACTTCTCGTACAGCTCGGCGATCACCTGCTGCTTGCCCTCGGCGCTGGTGACCTCGCCGGCGCGCCGTCGCACCGATTCGTAAAAGCCTTCCAACCGAGCGGTTTCGGCCTCCAGGCCGGCACCCCCGACGGTGTCGACCATCTTCTGCATGGCCCGCGACACCGGGTTGTGCGACGCGAAGTCATGCCCGGCGAACAGCGCGTCGAACACCGGCTTGGTGATCAGGTGCTGCGAGAGCATGCTGATCGCGTCATCGGGGGTGATCGAGTCATTGAGGTTATCGCGCAGCCCGGCCAGGAACTGCTCGAACGCCGCCGCCGCCGTAGCGTCGGCGCCGCCGAGCAGGGCGTGGATACGGGTGGTCAGCGTCGCGGCGATGTCGGCGACATCGGCGGCCCACTGCTCCCAATAGGTCCGGGTGCCAACCTTGTCGACGATGCGCGCGTAGATCGCTTCCTGCCACTGCGACAACGAGAACATCGCCAACTGCTCCGCGACGGCGGGTCCCGCCTCGTCGGAGGTCGGCCCGATGTGACCGCCCAACAGCTTGTCGCTGCCTTCACCGGTCTTCGTCGGCTTCACGTTCAGCGCAATGCTGTTCACCATCGCGTCGAAGCGCTCGTCGTGCGACCGCAACGCGTTGAGGACCTGCCACACCACCTTGAACCGTTTGTTGTCGGCCAACGCGGCAGACGGCTCGACACCCTCGGGCACCGCCACCGGCAAGATGACGTACCCGTAGTCCTTGCCGGGCGACTTGCGCATCACCCGACCGACCGACTGCACCACGTCGACGATGGAATTGCGCGGATTCAGGAACAGCACCGCGTCCAGCGCGGGCACGTCGACCCCTTCGGAGAGGCAGCGGGCGTTGGACAGGATGCGGCATTCATCCTCGGCGACCACGCCTTTGAGCCAGGCCAGCTGTTCGTTGCGGACCAGCGCGTTGAACGTCCCGTCCACGTGGCGCACCG"
])
panel = self.pg.create(v)
assert "TGGTGACGCGGGAGTAGAACGATCGCCAAGTGGTCGGTCTTGGCTGCCCACTTCATCCCCGGCGCCACCGGCAGGTCTCGCGGTCATCTCGACCAACGGAGGGCCGTCGGTGGTTCGTATCCGGCCAAGAACGGCGAGAACGGTTTGTGCCTCTATGCCAGGGTGAATGTCTCATCTCCCAGGCGGACGGTGATATCCAGTTCTCCGCCAAGAGCGGACACGTATTTGCGCAGTGTGTTGACCTGTGCGGAGCCGATGTCGCCGTTCTCGATGCTGGATACCCGGCTCTGCCGGATGTGCGCCAGCGCAGCCACCTGGACCTGGGTGAGTGACTGAGCCGCGCGCAGCTCCCGGAGCCGGAATGCCCGCACTTCATCGCGCATTCGTGCCTTGTGCCGGTCCACCGCCTCCCGGTTAACGGGACGTACGGCGTCCATGTCCCGTAGTGTCATCGCCATCGTGCCACTTACCCTTTCTTGCGCTTGCGCCTCTTTGGCTTCGTGTCCTCGAACTGTGCGAGATGTTCGGCAAACATCTCATCGGCCGCTTTGATCTTCTCGTCGTACCACTGGGTCCACCGCCCGGCCTTGTTACCGGCGGCCAGCATGATCGCCTGCCGCGCCGGGTCGAAGGCGAACAGAATGCGGACCTCGGACCGCCCTTGTGATCCTGGACGCAGCTCCTTCATGTTCTTGTGGCGCGACCCACGCACCGTGTCCACCAGAGGACAGCCAAGTGCGGGGCCCTCTTCCTCGAGAACCTCGATAGCTGCGAACACCAATTCGTAGGTCTCTCGGTCCAAGCCGTTGAGCCAGGCGGAGATGCGCTCCACATCCGCCGTCCACCCCACAGAGTCGCAGAGTAGCGCGATACGCGATATCACACAAGGGTGATATTCCTCCGGGTAAGAGCAGCGGGCGACGGGGCTACCGTCGAGGAAATGCCGGCAGGCGAGGACGGACTCTGCGCACCCGGGCCGTTGAAACAGTAGCCTGTGCCAGGCCGAGAATTCATCCCCACGTATGAGGCAGTACAGTGCGCCGCCGTGCGCGTTCTCCCATGGAACGTTCACGGGCTCCCGTGGATGACAGGCGTTTCATGAACGCCAGCGCCGCCGCAACCCGACCGAAAGCGGTTGACCCCAAGGAGAGCTGGAAGTCGAGGCCACCACCTTCGCCGCGGAGTTGCTCATGCCCGAGAGCGAGACTCGTCCCGAAATACGCCGGCTCGATTTCGGCAAGTTGCTCGAACTGAAGCGGGAATGGGCGTCGACCCGCTCGACCAGCCCCAGCCGGGTGACCAGCCCCAGCCGGGTGACCAGCCGATGCACCGCGGCGATCCCACCGAAGCCGGTGGCATCGATGTTGGCGCCGACCTCGTAGCGCACCGCGCCCGAACCCAGCATCGGCCTGGGCTGCGCCGCCCAGCGTCCAGCCCGCGCGTGCCGCGCCGCCACCCTGCGCCCTCGGCGTGTGATGTTTCGCCGACTCTGTTCATGGGTTATCTTCTTCACCACAAAGGCCTTTCCTGCTGGGCTGTGTTGAGGTCGCAAACCCAGCCAGGGTAAGGCCTTTGGCCTCTCCTACCCGGCCGACACGCTTACTGAAGGCCTAGTCTAGGCAGGCCATTCAATCTGCGGAATCGAAAAATTCGGTTCCAGCCTGCTCGTTTCCTTTCCGACAGCGATCTGACGTTGCGTAACGTCATTTGTACGGACTCTTTTAGCGGCATTGATTTCAGATGCCAACGCCGTCTGTGCTGTAGCGCCGATTGGCCGAAACTGTAAATTTGTATGATTATTTAAATCTTTGACGAACACGCGCCACAAACGTACTATCTCTTTGGCAAAGTCCACCGGCATCTCATTCAACGGTTTTGTTTGCGCGTGGTCGTCATATGTTGGTAACTGTGTAACCGGCCGCCTATCTTGCGCGTGCATCATATGACTATGAATCGGCCTTCTCCAGTGAAATTGATACAAGATCGATCCGATAAGCGGTACCTTGTACACAGTGCAATTGTAGTAATTCGCGTTTTGTCCTACGCTTGTATTCTGCGTGAAGAATTCAAACACG" in panel.refs
assert panel.alts == [
"GACCGCCGAGTGCGGCTGGATTGGATTTCACAAGGATGCCAATATCCGGCGCAACGCCGTCGAGCGACGGACGGTGCTCGACACGGGAGCCCGGCTATTCTGTGTGCCGCGGGCCGACATCCTGGCAGAGCAAGTCGCGGCACGGTATATTGCGTCCCTTGCGGCGATTGCCCGTGCCGCACGATTTCCGGGACCATTCATCTACACGGTTCACCCGAGCAAGATCGTTCGCGTGCTCTAGTCGTTCATCGCTCCGTTAACCGCCGGCGAGGCCGTCGACGATCTTCATGGTCTCGACGCTGACGGTGGTCACCTTCTTGATGAGGTCGACGATGTAGGTGGGATCGTCGTGTTCGTCGCACCAGTCGTTGGGGTCGTTGACGATGCCCGACGCTTTGTCGGTGGTGACGCGGTAGCGCTCGATGATCCAGCCGAGCGCCGAGCGGGAGCGAGCAGGTAGCGCTCGGCCTCGTCGGGAATGCCGGCGATGGTGACACGCGAGTTGTAGATGATCGTTGAGTGGTCTTGCTTGGACTTCCATTTCATCTTTTCGACGCGCCAGGTCTCGCGGTCCTCCGGATCTGCGCCCGGTTTGAGTTGCACATCAAGGGGATACGGCTTGACCGACTCGTAGCCGACATGTAAGTCGGCTAGTTTCCGGCCGGCGCTGGCGAGCTGGTCGAAGCGTTCGCGGGTCTCCGGTGTTGGGATGTGCGGGAGCATCTTCTTGAGGTCAGCGGCGTATTTTGTGCGGTAGGCGGGGTCATGCAGCAGGCCGTAGACGTAGTAGAAGATGTCGTCTTTGGTGACTTGGTCGCCGATCGTGTCGCGGTAGAGCTTGAGGATGACGCCGGTGATGTTGTCGACGCGGCGGTAGCCGTGGTCGTCTACTTCGGCGTTGGTGGTGGACTCGAAATCGAGTTCGCCGTCACGTGGTTCGGTCTTCTCGTAGGTCCAGCGCGGGAAGAATTGACCGTTGCTTGAGCCCCAGAATGCGAGATCGGGGATAGCGTTTAGCATCAGACACGAGAAGGGCTTGTCTGAGCCCATGCCAACCACGTAGTAACCGACATTCCCGTGCTCCGGCGTCGGAAACATCGACGGAAGCTGGTAGGTACAGTTGTTGAGCTGCTGGTTGGGGTCGAGGTAGGCGTGCTCTTTCGTAAATGGTCGGTACGTGCCGAGCCGCATTCCCGCGGGAGCGAATTCGATGCGAATGCCTTGTGCCACTTGCCGCTTGTTGATGCGGTCCCAGCTGAACTTGGCCGAGTCCACGGTAATGAGGGCGTCAACCGGCGGGGTCTTGGCGTCCCTTCCGCGGATCTCGTTGATCCGGTCGACCTCCGAGTTGTAGAAGTCGATCGTGCGTCCGATGTTGGCCTCGAGCGCACCACGTGAAAAGTTGTAACACCACGCATCCCGGCTGGTCTTCAAGCCCGCGGAATAGTTCGCGAAGACACGTGTCACGTCAAGAGCAGCCTTCTTGTCGCCGATAACCGGCCACGCGCTGAACGCGTCGTCGCGTTGGTTGACCCAGTCACCGTGCAAGTTGGGTGTGACTGTCTGCCATTCCACCGTGTCGAGGTAGCCGTCGCCGACGATCCGCAACTTCTCCTCGCGACTCAGGTAATCGCCGATGTCGCGGTAAAGGACATCGCATGGCCCGCTGTGCTTCGGATCCTTGATGCCAAGGAAGATCGCCACCGTGTTGCGACTCCCCCCGCCAAAGACCTTGCCGCCTTCCTGGCGTGAGAGTTCCCCAGCTGTGCGCTGGTTCCCCCGCAGGTTGTACACATATACCGCCGCGTAGTCGTCGGCGAGCGACAACCGCATGCCGTCTGCCGTGTTGCCGTCTATGTACCCACCATTGGAGACGAATCCGACAACACCGTTGTCACCAATGCGGTCGGTCGCCCACCGGAACGCGCGAATATACGAGTCGTACAGGCTGTTCTTCAGCTGCGCCGTCGACCGCTTCGCGTACGTCTGCTCAATCCGCCCGTCCAACGTCGGATACTTCACGTTGGCGTTCAGGTCGTTCGCGCTGCTCTGCCCCACCGAGTACGGCGGATTCCCGATGATCACGCTGATCGGCGTCGCCAGCTGTCGCAAGATCCGAGCGTTGTTGTACGGGAACATGATCGCGTCCATCGAGTCCCCGGCTTCGGAAATCTGGAACGTGTCGGCCAGCGCCATCCCGGGGAACGGCTCATAGGCGTCGGCGTCGGCGGTCTTGCCCGCCAAAGCATGGTAGGTCGACTCGATGTTCACCGCGGCGATGTAGTACGCCAGCAGCATGATCTCGTTGGCGTGCAGCTCTTGCGAGTACTTTCGGGTGAGGTCGGCGGCCGTGATCAGGTCGGACTGCAGCAGCCGGGTAATGAATGTGCCCGTCCCGGCGAAGCCGTCCAGAATATGCACGCCCTCGTCGGTCAGCCCGCGCCCGAAATGCTTGCGCGACACGAAATCAGCCGCCCGCACAATGAAGTCCACGACCTCGACCGGCGTGTACACGATCCCCAGCGCCTCGGCCTGCTTCTTGAAGCCGATGCGGAAGAACTTCTCGTACAGCTCGGCGATCACCTGCTGCTTGCCCTCGGCGCTGGTGACCTCGCCGGCGCGCCGTCGCACCGATTCGTAAAAGCCTTCCAACCGAGCGGTTTCGGCCTCCAGGCCGGCACCCCCGACGGTGTCGACCATCTTCTGCATGGCCCGCGACACCGGGTTGTGCGACGCGAAGTCATGCCCGGCGAACAGCGCGTCGAACACCGGCTTGGTGATCAGGTGCTGCGAGAGCATGCTGATCGCGTCATCGGGGGTGATCGAGTCATTGAGGTTATCGCGCAGCCCGGCCAGGAACTGCTCGAACGCCGCCGCCGCCGTAGCGTCGGCGCCGCCGAGCAGGGCGTGGATACGGGTGGTCAGCGTCGCGGCGATGTCGGCGACATCGGCGGCCCACTGCTCCCAATAGGTCCGGGTGCCAACCTTGTCGACGATGCGCGCGTAGATCGCTTCCTGCCACTGCGACAACGAGAACATCGCCAACTGCTCCGCGACGGCGGGTCCCGCCTCGTCGGAGGTCGGCCCGATGTGACCGCCCAACAGCTTGTCGCTGCCTTCACCGGTCTTCGTCGGCTTCACGTTCAGCGCAATGCTGTTCACCATCGCGTCGAAGCGCTCGTCGTGCGACCGCAACGCGTTGAGGACCTGCCACACCACCTTGAACCGTTTGTTGTCGGCCAACGCGGCAGACGGCTCGACACCCTCGGGCACCGCCACCGGCAAGATGACGTACCCGTAGTCCTTGCCGGGCGACTTGCGCATCACCCGACCGACCGACTGCACCACGTCGACGATGGAATTGCGCGGATTCAGGAACAGCACCGCGTCCAGCGCGGGCACGTCGACCCCTTCGGAGAGGCAGCGGGCGTTGGACAGGATGCGGCATTCATCCTCGGCGACCACGCCTTTGAGCCAGGCCAGCTGTTCGTTGCGGACCAGCGCGTTGAACGTCCCGTCCACGTGGCGCACCGAACACGCCAGGCCCGGGCCGTCGTCAACCAATTCGCGGTATGCCTCAACCACTTTCGGGAACAGCTCGGCAACCTGCTTGGACGTCTTGATGTCCTTGGCGAACGCCACCGCCCGACGCATCGGCGGCTCACCGGCGACAATGCCGGTACCGGACCGCTTGGCCAGGCCATTCCAGCAGCCGACGATCTTGGAGGCGTCGTCGAGCATCAGCTCGCCGGAAACCCCGGAGAGTTCCTGCTGCAACCGGGGCGCGATCACGCCCTGATCGACGGTGAGCACCATCACCTTGTAGTCGGTGAGCAGCCCGCGCTCCACCGCCTCGCCGAACGACAGCCGGTGAAACTCCGGCCCGAACGTCAGCTCGTCGTCCATCGACACCAACTCGGCGGAGTGCTGGTCGGCCCTGTCCTTGATGCTCTCGGTGAAAATCCTTGGCGTGGCGGTCATATACAGCCGCCGGGCCGCCTTCAGATACTGACCGTCGTGCACCCGC"
]
def run(parser, args):
DB = connect('atlas-%s' % (args.db_name))
if DB is not None:
try:
Variant.objects()
logging.info("Connected to atlas-%s" % (args.db_name))
except (ServerSelectionTimeoutError, ConnectionError):
DB = None
logging.warning(
"Could not connect to database. Continuing without using genetic backgrounds"
)
mutations = []
reference = os.path.basename(args.reference_filepath).split('.fa')[0]
if args.vcf:
run_make_probes_from_vcf_file(args)
elif args.genbank:
aa2dna = GeneAminoAcidChangeToDNAVariants(args.reference_filepath,
args.genbank)
if args.text_file:
with open(args.text_file, 'r') as infile:
reader = csv.reader(infile, delimiter="\t")
for row in reader:
gene, mutation, alphabet = row
if alphabet == "DNA":
protein_coding_var = False
else:
protein_coding_var = True
for var_name in aa2dna.get_variant_names(
gene, mutation, protein_coding_var):
mutations.append(
Mutation(reference=reference,
var_name=var_name,
gene=aa2dna.get_gene(gene),
mut=mutation))
else:
for variant in args.variants:
gene, mutation = variant.split("_")
for var_name in aa2dna.get_variant_names(gene, mutation):
mutations.append(
Mutation(reference=reference,
var_name=var_name,
gene=gene,
mut=mutation))
else:
if args.text_file:
with open(args.text_file, 'r') as infile:
reader = csv.reader(infile, delimiter="\t")
for row in reader:
gene_name, pos, ref, alt, alphabet = row
if gene_name == "ref":
mutations.append(
Mutation(reference=reference,
var_name="".join([ref, pos, alt])))
else:
mutations.append(
Mutation(reference=reference, var_name=row[0]))
else:
mutations.extend(
Mutation(reference=reference, var_name=v)
for v in args.variants)
al = AlleleGenerator(reference_filepath=args.reference_filepath,
kmer=args.kmer)
for enum, mut in enumerate(mutations):
if enum % 100 == 0:
logger.info(
"%i of %i - %f%%" %
(enum, len(mutations), round(100 * enum / len(mutations), 2)))
variant_panel = make_variant_probe(al,
mut.variant,
args.kmer,
DB=DB,
no_backgrounds=args.no_backgrounds)
if variant_panel is not None:
for i, ref in enumerate(variant_panel.refs):
try:
gene_name = mut.gene.name
except AttributeError:
gene_name = "NA"
sys.stdout.write(
">ref-%s?var_name=%s&num_alts=%i&ref=%s&enum=%i&gene=%s&mut=%s\n"
% (mut.mut, mut.variant.var_name, len(variant_panel.alts),
mut.reference, i, gene_name, mut.mut))
sys.stdout.write("%s\n" % ref)
for i, a in enumerate(variant_panel.alts):
sys.stdout.write(
">alt-%s?var_name=%s&enum=%i&gene=%s&mut=%s\n" %
(mut.mut, mut.variant.var_name, i, gene_name, mut.mut))
sys.stdout.write("%s\n" % a)
else:
logging.warning("All variants failed for %s_%s - %s" %
(mut.gene, mut.mut, mut.variant))
class TestINDELandSNPSAlleleGenerator():
def setUp(self):
DB.drop_database('atlas-test')
self.pg = AlleleGenerator(
reference_filepath="atlasvar/data/BX571856.1.fasta")
self.pg2 = AlleleGenerator(
reference_filepath="atlasvar/data/NC_000962.2.fasta")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file",
reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref",
md5checksum="sre",
reference_sets=[
self.reference_set])
def test_ins_with_SNP_context(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["ATTT"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
panel = self.pg.create(v, context=[v2])
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCATTTATCAAATTTCATAACATCACCATGAGTTTGAT",
"CGATTAAAGATAGAAATACACGATGCGAGCATTTTTCAAATTTCATAACATCACCATGAGTTTGAT"])
def test_del_with_SNP_context1(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AA",
start=31,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=33,
alternate_bases=["A"])
panel = self.pg.create(v, context=[v2])
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCATCAAATTTCATAACATCACCATGAGTTTGATC",
"CGATTAAAGATAGAAATACACGATGCGAGCAACAAATTTCATAACATCACCATGAGTTTGATC"])
def test_del_with_SNP_context2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AA",
start=31,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["T"])
panel = self.pg.create(v, context=[v2])
assert self.pg._remove_overlapping_contexts(v, [v2]) == []
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT" in panel.refs
assert sorted(
panel.alts) == sorted(
["CGATTAAAGATAGAAATACACGATGCGAGCATCAAATTTCATAACATCACCATGAGTTTGATC"])
def test_del_with_ins_context1(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AAT",
start=31,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=4,
alternate_bases=["TTTT"])
panel = self.pg.create(v, context=[v2])
assert self.pg._remove_overlapping_contexts(v, [v2]) == [v2]
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCACAAATTTCATAACATCACCATGAGTTTGATCC",
"CGATTTTTAAAGATAGAAATACACGATGCGAGCACAAATTTCATAACATCACCATGAGTTTGAT"])
def test_del_with_ins_context2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=1,
alternate_bases=["CTTT"])
panel = self.pg.create(v, context=[v2])
assert self.pg._remove_overlapping_contexts(v, [v2]) == [v2]
assert self.pg._remove_contexts_not_within_k(v, [v2]) == []
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC" in panel.refs
assert sorted(
panel.alts) == sorted(
["CGATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC"])
def test_del_with_ins_context3(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=5,
alternate_bases=["TT"])
panel = self.pg.create(v, context=[v2])
assert self.pg._remove_overlapping_contexts(v, [v2]) == [v2]
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC",
"GATTTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC"])
def test_del_with_ins_context4(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=5,
alternate_bases=["TT"])
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=5,
alternate_bases=["TG"])
panel = self.pg.create(v, context=[v2, v3])
assert self.pg._remove_overlapping_contexts(v, [v2, v3]) == [v2, v3]
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC",
"GATTTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC",
"GATTGAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC"])
def test_del_with_ins_context5(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=5,
alternate_bases=["TT"])
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=6,
alternate_bases=["AG"])
panel = self.pg.create(v, context=[v2, v3])
assert self.pg._remove_overlapping_contexts(v, [v2, v3]) == [v2, v3]
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC",
"GATTTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC",
"GATTAGAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC",
"GATTTAGAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATC"])
def test_del_with_ins_context_where_base_is_deleted(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=33,
alternate_bases=["C"])
panel = self.pg.create(v, context=[v2])
assert self.pg._remove_overlapping_contexts(v, [v2]) == []
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC" in panel.refs
assert sorted(
panel.alts) == sorted(
["CGATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC"])
def test_del_with_ins_context_where_base_is_deleted2(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="TAAA",
start=5,
alternate_bases=["T"])
v3 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=7,
alternate_bases=["AG"])
panel = self.pg.create(v, context=[v2, v3])
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC",
"CGATTGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCCAAA",
"GATTAAGAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC"])
panel = self.pg.create(v, context=[v3, v2])
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC" in panel.refs
assert sorted(
panel.alts) == sorted(
[
"CGATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC",
"CGATTGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCCAAA",
"GATTAAGAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC"])
def test_snp_with_replace_context(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="G",
start=2338961,
alternate_bases=["A"])
v1 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="GGATG",
start=2338990,
alternate_bases=["CGATA"])
panel = self.pg2.create(v, context=[v1])
assert "CGACTAGCCACCATCGCGCATCAGTGCGAGGTCAAAAGCGACCAAAGCGAGCAAGTCGCGGAT" in panel.refs
assert panel.alts == \
["CGACTAGCCACCATCGCGCATCAGTGCGAGATCAAAAGCGACCAAAGCGAGCAAGTCGCGGAT",
"CGACTAGCCACCATCGCGCATCAGTGCGAGATCAAAAGCGACCAAAGCGAGCAAGTCGCCGAT"]
def test_indel_snp_indel_context(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="TCGCGTGGC",
start=4021459,
alternate_bases=["GCGAGCAGA"])
v1 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=4021455,
alternate_bases=["ATCTAGCCGCAAG"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="T",
start=4021489,
alternate_bases=["G"])
panel = self.pg2.create(v) # , context = [v1, v2])
assert "ATCATGCGATTCTGCGTCTGCTCGCGAGGCTCGCGTGGCCGCCGGCGCTGGCGGGCGATCTCG" in panel.refs
panel = self.pg2.create(v, context=[v1, v2])
assert sorted(
panel.alts) == sorted(
[
"ATCATGCGATTCTGCGTCTGCTCGCGAGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCTCG",
"ATCATGCGATTCTGCGTCTGCTCGCGATCTAGCCGCAAGGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCTCG",
"ATCATGCGATTCTGCGTCTGCTCGCGAGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCGCG",
"ATCATGCGATTCTGCGTCTGCTCGCGATCTAGCCGCAAGGGCGCGAGCAGACGCCGGCGCTGGCGGGCGATCGCG"])
def test_complex_context(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATTT",
start=1503643,
alternate_bases=["A"])
v1 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="CCT",
start=1503615,
alternate_bases=["C"])
v2 = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=1503655,
alternate_bases=["ATGCCGCCGCC"])
panel = self.pg2.create(v, context=[v1, v2])
assert "ATCCTGGAGCCCACCAGCGGAAACACCGGCATTTCGCTGGCGATGGCGGCCCGGTTGAAGGGG" in panel.refs
assert panel.alts == [
"CATCCTGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGGCGGCCCGGTTGAAGGGGTA",
"CCATCGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGGCGGCCCGGTTGAAGGGGTAC",
"ATCCTGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGCCGCCGCCTGGCGGCCCGGTTGAAGGGG",
"ATCGGAGCCCACCAGCGGAAACACCGGCACGCTGGCGATGCCGCCGCCTGGCGGCCCGGTTGAAGGGG"]
class TestINDELAlleleGenerator():
def setUp(self):
DB.drop_database('atlas-test')
self.pg = AlleleGenerator(
reference_filepath="atlasvar/data/BX571856.1.fasta")
self.pg2 = AlleleGenerator(
reference_filepath="atlasvar/data/NC_000962.2.fasta")
self.reference_set = ReferenceSet().create_and_save(name="ref_set")
self.variant_set = VariantSet.create_and_save(
name="this_vcf_file", reference_set=self.reference_set)
self.variant_sets = [self.variant_set]
self.reference = Reference().create_and_save(
name="ref", md5checksum="sre", reference_sets=[self.reference_set])
def test_simple_deletion1(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AA",
start=31,
alternate_bases=["A"])
assert v.is_indel
assert v.is_deletion
panel = self.pg.create(v)
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT" in panel.refs
assert self.pg._calculate_length_delta_from_indels(v, []) == 1
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCATCAAATTTCATAACATCACCATGAGTTTGATC"
]
def test_simple_deletion2(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AT",
start=32,
alternate_bases=["A"])
panel = self.pg.create(v)
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC" in panel.refs
assert panel.alts == [
"GATTAAAGATAGAAATACACGATGCGAGCAACAAATTTCATAACATCACCATGAGTTTGATCC"
]
def test_simple_deletion3(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AT",
start=2902618,
alternate_bases=["T"])
panel = self.pg.create(v)
assert "TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTAT" in panel.refs
assert panel.alts == [
"ATAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTT"
]
def test_simple_deletion4(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="ATC",
start=32,
alternate_bases=["A"])
panel = self.pg.create(v)
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC" in panel.refs
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCAAAAATTTCATAACATCACCATGAGTTTGATCC"
]
def test_simple_insertion1(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=1,
alternate_bases=["TTTC"])
panel = self.pg.create(v)
assert v.is_indel
assert v.is_insertion
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT" in panel.refs
assert panel.alts == [
"TTTCGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT"
]
def test_simple_insertion2(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="C",
start=1,
alternate_bases=["CTTT"])
panel = self.pg.create(v)
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT" in panel.refs
assert panel.alts == [
"CTTTGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT"
]
def test_simple_insertion3(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=31,
alternate_bases=["ATTT"])
panel = self.pg.create(v)
assert "CGATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGAT" in panel.refs
assert panel.alts == [
"CGATTAAAGATAGAAATACACGATGCGAGCATTTATCAAATTTCATAACATCACCATGAGTTTGAT"
]
def test_simple_insertion4(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=32,
alternate_bases=["AGGGG"])
panel = self.pg.create(v)
assert "GATTAAAGATAGAAATACACGATGCGAGCAATCAAATTTCATAACATCACCATGAGTTTGATC" in panel.refs
assert panel.alts == [
"GATTAAAGATAGAAATACACGATGCGAGCAAGGGGTCAAATTTCATAACATCACCATGAGTTTGATC"
]
def test_simple_insertion5(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=2902618,
alternate_bases=["ATGC"])
panel = self.pg.create(v)
assert "TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTAT" in panel.refs
assert panel.alts == [
"TAACAAAATCCTTTTTATAACGCAAGTTCATTTTATACTACTGCTCAATTTTTTTACTTTTATGCT"
]
def test_double_insertion(self):
v = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="A",
start=4021408,
alternate_bases=["ACGCTGGCGGGCG"])
v1 = Variant.create(variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="AGA",
start=4021406,
alternate_bases=["CGG"])
context = [v1]
assert self.pg2._remove_overlapping_contexts(v, [v1]) == []
panel = self.pg2.create(v, context=context)
assert "ATCTAGCCGCAAGGGCGCGAGCAGACGCAGAATCGCATGATTTGAGCTCAAATCATGCGATTC" in panel.refs
assert panel.alts == [
"ATCTAGCCGCAAGGGCGCGAGCAGACGCAGACGCTGGCGGGCGATCGCATGATTTGAGCTCAAATCATGCGATTC"
]
def test_large_insertion(self):
v = Variant.create(
variant_sets=self.variant_sets,
reference=self.reference,
reference_bases="CCGCCGGCCCCGCCGTTT",
start=1636155,
alternate_bases=[
"CTGCCGGCCCCGCCGGCGCCGCCCAATCCACCGAAGCCCCTCCCTTCGGTGGGGTCGCTGCCGCCGTCGCCGCCGTCACCGCCCTTGCCGCCGGCCCCGCCGTCGCCGCCGGCTCCGGCGGTGCCGTCGCCGCCCTGGCCGCCGGCCCCGCCGTTTCCG"
])
panel = self.pg2.create(v, context=[])
assert "AGACCTAGCAGGGTGCCGGCGCCGCCCTTGCCGCCGGCCCCGCCGTTTCCGCCGCCGCCATCG" in panel.refs
assert panel.alts == [
"GGTTGGATCGCCACCGGCGCCACCGGCGCCGCCCGCGCCACCAGCACCGCCGCTGCCATCTGGGTCCGTCGAGTCGCCGAGGACGCCGGCGCCGCCATTGTCGCCAAATACCGTGAGACCTAGCAGGGTGCCGGCGCCGCCCTTGCTGCCGGCCCCGCCGGCGCCGCCCAATCCACCGAAGCCCCTCCCTTCGGTGGGGTCGCTGCCGCCGTCGCCGCCGTCACCGCCCTTGCCGCCGGCCCCGCCGTCGCCGCCGGCTCCGGCGGTGCCGTCGCCGCCCTGGCCGCCGGCCCCGCCGTTTCCGCCGCCGCCGCCATCGCCGATGATGTTTTCCCCGCCCTTGCCGCCAGCCCCAGCGTTCCCGCCGGCTCCGCCACTGGCGCCGGTGCCGCCGGGTGCAACGGCGTTGGCGCCGTTACCGCCGTTGCCGCCTTT"
]